Minor fix

gga_run_workflow_phaeo_jbrowse.py

@@ -450,12 +450,13 @@ if __name__ == "__main__":
                     root_url = "https://{0}".format(config[constants.CONF_ALL_HOSTNAME])
                 else:
                     root_url = config[constants.CONF_JBROWSE_MENU_URL]
+                # Set "Genus" and "species" as they are given in the add_organism tool (with spaces replaced by "_")
                 species_strain_sex = org_wf_param.chado_species_name.replace(" ", "-")
-                jbrowse_menu_url = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species_strain_sex}/mRNA/{id}".format(
+                jbrowse_menu_url = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(
                     root_url=root_url,
                     genus_sp=genus_species,
                     Genus=org_wf_param.genus_uppercase,
-                    species_strain_sex=species_strain_sex,
+                    species=species_strain_sex,
                     id="{id}")
                 # Replace values in the workflow dictionary
                 workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_JBROWSE]["tool_state"] = \
@@ -568,19 +569,20 @@ if __name__ == "__main__":
                     root_url = "https://{0}".format(config[constants.CONF_ALL_HOSTNAME])
                 else:
                     root_url = config[constants.CONF_JBROWSE_MENU_URL]
+                # Set "Genus" and "species" as they are given in the add_organism tool (with spaces replaced by "_")
                 species_strain_sex_org1 = sp_wf_param_org1.chado_species_name.replace(" ", "-")
                 species_strain_sex_org2 = sp_wf_param_org2.chado_species_name.replace(" ", "-")
-                jbrowse_menu_url_org1 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species_strain_sex}/mRNA/{id}".format(
+                jbrowse_menu_url_org1 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(
                     root_url=root_url,
                     genus_sp=genus_species,
                     Genus=sp_wf_param_org1.genus_uppercase,
-                    species_strain_sex=species_strain_sex_org1,
+                    species=species_strain_sex_org1,
                     id="{id}")
-                jbrowse_menu_url_org2 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species_strain_sex}/mRNA/{id}".format(
+                jbrowse_menu_url_org2 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(
                     root_url=root_url,
                     genus_sp=genus_species,
                     Genus=sp_wf_param_org2.genus_uppercase,
-                    species_strain_sex=species_strain_sex_org2,
+                    species=species_strain_sex_org2,
                     id="{id}")
                 # Replace values in the workflow dictionary
                 workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"] = \